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Hi, One thing here is that your input data has not been prepared correctly - some of the subjects clearly have incorrect voxel dimensions! It also looks like some subjects (e.g., total19520_FA) have some artefacts in them (much brighter slices in some places). I'm also confused by the registrations in all_FA - they do indeed look much too big. When I ran tbss_2_reg with just the -T option on your first subject it gave sensible results - did you run a different registration option? Cheers, Steve. On 16 Oct 2007, at 05:38, Marc Dubin wrote: > Hi, > > The overlay of the individual FA files with FMRIB58_FA seems to be > good but there may be a problem with all_FA - there is a large part > of the frontal lobe bilaterally that got cut out, I think during > the nonlinear transformation to FMRIB58_FA. The 31 files for the 31 > individual subjects are included as well as all_FA in 542195. > > Best, > Marc > > On 10/15/07, Steve Smith <[log in to unmask] > wrote:Hi - I'm > suprised that you get this with the -T option. If you load > in all_FA first into FSLView, and then overlay the FMRIB58_FA > (threshold this, change its colour to red-yellow, and make it a > little transparent) and then move through the timepoints, do all > subjects behave in a similar way to what you've described? > > We can have a look and advise on what's happening; > Please upload the files in a single compressed tarfile to > http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi > and then email me the upload ID. > > Cheers. > > > > On 15 Oct 2007, at 02:36, Marc Dubin wrote: > > > Hello FSL Users, > > > > Using the TBSS tools I have been carrying out the tbss_2_reg step > > with the -T option (FMRIB58_FA). I > > then go through all of the remaining steps of TBSS and then when I > > visualise with: > > > > fslview MNI152 mean_FA_skeleton -l Green -b 2000,8000 tbss_tstat1 - > > l Red-Yellow -b 3,6 > > tbss_tstat2 -l Blue-Lightblue -b 3,6 > > > > the mean_FA_skeleton significantly overshoots the brain, > > terminating in or even beyond the skull > > (the overall extent of the skeleton is significantly larger that > > the brain). > > > > Any ideas about what might be going on here would be greatly > > appreciated! > > > > Thanks, > > Marc > > > ---------------------------------------------------------------------- > -- > --- > Stephen M. Smith, Professor of Biomedical Engineering > Associate Director, Oxford University FMRIB Centre > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 222726 (fax 222717) > [log in to unmask] http://www.fmrib.ox.ac.uk/ ~steve > ---------------------------------------------------------------------- > -- > --- > > > > -- > Marc Dubin, MD PhD > Resident in Psychiatry - PGY4 > Weill Cornell Medical College > > 212-746-3764 (w) 646-831-8886 (c) ------------------------------------------------------------------------ --- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ------------------------------------------------------------------------ ---